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- EMDB-64188: structure of a 12 base pair Rad51 D-loop complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64188
Titlestructure of a 12 base pair Rad51 D-loop complex
Map data
Sample
  • Complex: mRAD51 D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (48-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (35-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordshomologous recombination / strand exchange / D-loop / RECOMBINATION / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly ...Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / synaptonemal complex / cellular response to cisplatin / DNA strand invasion / mitotic recombination / cellular response to hydroxyurea / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / lateral element / DNA strand exchange activity / regulation of DNA damage checkpoint / telomere maintenance via recombination / reciprocal meiotic recombination / single-stranded DNA helicase activity / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / cellular response to alkaloid / nuclear chromosome / replication fork processing / response to X-ray / ATP-dependent activity, acting on DNA / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / telomere organization / condensed nuclear chromosome / cellular response to ionizing radiation / meiotic cell cycle / cellular response to gamma radiation / PML body / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to toxic substance / single-stranded DNA binding / chromosome / site of double-strand break / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLuo SC / Ho MC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-TP-113-L01 to M.C.H Taiwan
CitationJournal: Nat Commun / Year: 2025
Title: RAD51 D-loop structures reveal the mechanism of eukaryotic RAD51-mediated strand exchange.
Authors: Shih-Chi Luo / Cheng-Han Yang / Hsin-Yi Yeh / Cheng-Wei Lin / Min-Chi Yeh / Peter Chi / Meng-Chiao Ho /
Abstract: Strand exchange is a key step in homologous recombination, enabling template-based repair of DNA double-strand breaks. Eukaryotic RAD51 forms an ATP-dependent helical presynaptic filament on single- ...Strand exchange is a key step in homologous recombination, enabling template-based repair of DNA double-strand breaks. Eukaryotic RAD51 forms an ATP-dependent helical presynaptic filament on single-stranded DNA (ssDNA), which then searches for homologous double-stranded DNA (dsDNA), and catalyzes the strand exchange to form a D-loop in an ATP hydrolysis-independent manner. The molecular mechanism by which RAD51 facilitates dsDNA unwinding and pairing remains unclear. Here, we present cryo-EM structures of RAD51 mini-filaments bound to homologous dsDNA, capturing five intermediates from dsDNA recruitment to D-loop formation. These structures, together with molecular dynamics simulations, suggest a stepwise mechanism: the conserved N-terminal domain (NTD) recruits and bends the dsDNA, weakening base pairing near the exchange site. Subsequent engagement with positively-charged regions, including the loop L2 and loop Arg303-Arg306, further bends the homologous dsDNA, thereby not only positioning it closer to the strand exchange site but also inducing local base-pair opening. Additionally, the loop L2 (Met278 and Phe279) inserts between strands, and the secondary DNA binding sites (S2 sites) capture the displaced strand to prevent strand reannealing. Together, our findings provide detailed insight into a spatially coordinated mechanism of strand exchange by RAD51.
History
DepositionApr 15, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64188.png

Downloads & links

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Map

FileDownload / File: emd_64188.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-0.6645128 - 1.6989089
Average (Standard dev.)0.0041144 (±0.04562884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64188_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64188_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : mRAD51 D-loop

EntireName: mRAD51 D-loop
Components
  • Complex: mRAD51 D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (48-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (35-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: mRAD51 D-loop

SupramoleculeName: mRAD51 D-loop / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: mRAD51 protein filament in complex with dsDNA
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 39.55775 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KGADDDDKVP DPMAMQMQLE ASADTSVEEE SFGPQPISRL EQCGINANDV KKLEEAGYHT VEAVAYAPKK ELINIKGIS EAKADKILTE AAKLVPMGFT TATEFHQRRS EIIQITTGSK ELDKLLQGGI ETGSITEMFG EFRTGKTQIC H TLAVTCQL ...String:
MASWSHPQFE KGADDDDKVP DPMAMQMQLE ASADTSVEEE SFGPQPISRL EQCGINANDV KKLEEAGYHT VEAVAYAPKK ELINIKGIS EAKADKILTE AAKLVPMGFT TATEFHQRRS EIIQITTGSK ELDKLLQGGI ETGSITEMFG EFRTGKTQIC H TLAVTCQL PIDRGGGEGK AMYIDTEGTF RPERLLAVAE RYGLSGSDVL DNVAYARGFN TDHQTQLLYQ AEDMMVESRY AL LIVDSAT ALYRTDYSGR GELSARQMHL ARFLRMLLRL ADEFGVAVVI TNQVVAQVDG AAMFAADPKK PIGGNIIAHA STT RLYLRK GRGETRICKI YDSPCLPEAE AMFAINADGV GDAKD

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 2 / Details: 3'-tilt dsDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.720452 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DG)(DA)(DG) (DT)(DC)(DA)(DG)(DC)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DT)(DC)(DA)(DA)(DT)(DT)(DA) (DA) (DG)(DC)(DA)(DA)(DG)(DT)(DA)(DC)

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Macromolecule #3: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 3 / Details: 5'-tilt dsDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.85651 KDa
SequenceString:
(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC)(DT)(DT) (DA)(DA)(DT)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DG)(DT)(DG)(DG)(DG)(DC)(DG)(DA)(DC) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DA)(DC) (DT) (DC)(DG)(DA)(DC)(DA)(DC)(DC)(DG)

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Macromolecule #4: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 4
Details: ssDNA, the 3'-end contains extra eight nucleotides (T) that is built based on density map due to end to end fusion of Rad51.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.580766 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DG)(DT)(DC)(DG)(DC)(DC)(DC) (DA)(DC)(DG)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 9 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 9 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45865
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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